ST. LOUIS -- In Sunday's 16-13 overtime loss to the Rams, there were multiple layers of 49ers blame. In fact, there were enough to make a Kaepernick upside-down layer blame cake.

But let us begin with the top layer. You know, the khaki-pants-and-headset layer:

What the heck was head coach Jim Harbaugh thinking?

What was his thought process at such a crucial moment, when he passed along such a dicey play call from offensive coordinator Greg Roman? The 49ers were protecting a 10-2 lead with 3:11 left in the fourth quarter. The offense faced a third-and-3 situation at its own 17-yard line.

And the call from Roman/Harbaugh? It was a complicated option play that required quarterback Colin Kaepernick to fake a handoff, then pitch the ball to Ted Ginn Jr. trailing behind. Kaepernick did as instructed. But he was hurried by a charging defender and instead launched the pitch more toward Kansas City than toward Ginn.

The ball hit the turf and was recovered by St. Louis cornerback Janoris Jenkins, who stormed into the end zone for a touchdown.

"I don't know what they were trying to accomplish there," said St. Louis coach Jeff Fisher, handily winning the day's award for understatement. "But we took advantage of one of their mistakes."

The Rams then immediately tied the game with a successful two-point conversion -- before going on to win in the extra period. The extra period never should have happened. And neither should the loss.

But say this much for Harbaugh. He didn't shirk blame. He owned the goof.

"That was on us," Harbaugh said of the option-pitch decision. "That was the wrong play to call at that time. I would love to have that one back. Don't blame the players on that one. It was too risky of a play at that time."

Kaepernick expressed guilt, anyway.

"I just pitched it high," he said. "It's my fault all the way. I should have played it safe. I should have just kept it, let the clock run, let our punter get on the field, let our defense play. It was just a bad pitch on my part."

No argument here. Yet it was still Harbaugh and Roman who put the pressure on Kaepernick, starting just his third NFL game, to execute the play with 100 percent certainty of not messing up.

That sort of decision-making and execution (by coaches and players) exemplified a day in which the 49ers defense performed well enough to win. Meanwhile, the special teams performed well enough for kicker David Akers (who also took blame) to miss a 51-yard field goal attempt in overtime. And the offense performed well enough to profoundly peeve tackle Joe Staley and center Jonathan Goodwin.

"We got 13 points on the board, and we need more than that," said Goodwin. "A couple of instances, we shot ourselves in the foot. But most games, including this one, are not won or lost on one play. Overall, too many negative plays hurt us."

Added Staley, who was mad at himself for a key holding penalty: "Late in the season, we shouldn't be having games like this. We've got to get this fixed. It seemed like everything that their defense called was the best call to have."

Staley's last observation, echoed by other 49ers players, was the most telling. It suggests that Fisher and the Rams were either stealing 49ers play calls (extremely unlikely) or that they had cracked the Kaepernick code. You knew that once he put some games on video for NFL defensive coordinators to vet and dissect, the second-year man from Nevada would be facing bigger challenges.

Welcome to NFL scouting-scheming, Colin.

Sunday, the Rams defensive plan called for better coverage of the deeper passes Kaepernick prefers to throw, causing him to hold onto the ball longer. St. Louis combined this with some creative containment that led to three sacks plus one intentional grounding penalty that was enforced as a safety (although replays showed the call was shaky). Official statistics showed that "under duress," Kaepernick completed 1 of 5 passes for 6 yards Sunday. Coming into the game, he was 9 for 17 "under duress."

"I have to play better," Kaepernick said. "There were plays that happened that I shouldn't have let happen ... be smart with the ball. Our defense played a great game. I gave up those points that were on the scoreboard for the Rams."

Of course, we know what's coming next. Harbaugh set up himself for second-guessing by choosing to start Kaepernick over veteran Alex Smith. So here it comes. But it is foolish to speculate on whether Smith might have made the same errors as Kaepernick on Sunday because the coaches would have called different plays for Smith -- including the option play, most likely.

Smith might have won Sunday's game with those different plays. Or the Rams might have stymied him, too.

Kaepernick did impressively rally from his mistakes, leading one scoring drive after giving up the safety and another one after his option-pitch fumble. But he also messed up by failing to stay inbounds after a scramble on the 49ers' final offensive possession in the fourth quarter. The possession produced a go-ahead field goal, but because Kaepernick went out of bounds on the previous play, he stopped the clock and gave the Rams more time to come back and tie the game themselves.

Fisher, the St. Louis coach, did not refrain from noting Kaepernick's error.

"I was expecting to get the ball back inside of a minute with no timeouts left," Fisher said. "Instead, we have it with (1:34) and a timeout left. So that certainly helped our cause."

Harbaugh said he was not contemplating a quarterback change next week. Kaepernick acknowledged that he learned a lot Sunday. The justifiable question to ask is whether you want to have your younger and more inexperienced quarterback undergo this education while a team is pushing down the tough home stretch to win a playoff spot.

There, however, the 49ers got lucky with Sunday's other NFL results. To clinch the NFC West title, the 49ers now need to win just two of their remaining four games -- as long as one of those victories is at Seattle on Dec. 23.

And what about the race for the NFC overall second seed, bringing with it a coveted first-round bye? The 49ers still own that, too. They possess a half-game lead in the standings over Chicago and Green Bay -- but it's effectively a game-and-a-half lead. The 49ers own tiebreaker advantages over the Bears and Packers because of head-to-head victories.

This doesn't mean Sunday's loss should be laughed off. It was an inexcusably lost opportunity. If the 49ers lose any more of them, they might be out of options. They should have been without one against the Rams.

Contact Mark Purdy at mpurdy@mercurynews.com. Follow him on Twitter at twitter.com/MercPurdy.

Sunday's game

Miami (5-7) at 49ers (8-3-1), 1:05 p.m. CBS

Scan: Use your smartphone to access a photo gallery from Sunday's game, or visit

mercurynews.com/49ers


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